Mammalian development is driven by the successive restriction of developmental potential as the totipotent zygote generates the diversity of mature cell types present within an adult animal. The characteristics adopted by each cell within the animal are stable and are carried as a long-term memory within that cell type. Most current models suggest that the mechanisms underlying cellular memory are epigenetic modifications of the genome. In mammals, methylation of cytosine nucleotides, mainly in CG dinucleotides sequences, forms an indisputable epigenetic mark that is copied at each cell division. During the development of germ cells, epigenetic marks are largely erased, essentially as a path toward resetting the genome to a totipotent state. After fertilization, the patterns of DNA methylation are again rewritten. We propose to use next-generation DNA sequencing technologies to map patterns of DNA methylation during the most dynamic phases of epigenetic programming and re-programming during mammalian development. We will correlate these with patterns of RNA expression through analyses of both long and short RNAs. The goal of this proposal is to understand how the deposition of epigenetic marks leads to the creation of the diversity of cell types within an adult organism and whether those marks themselves presage changes in the characteristics of cells that harbor them. Importantly, we will compare patterns of epigenetic modifications in early embryos derived from normal mice to epigenetic profiles of early embryos in hormone-treated, superovulated mothers. There are already indications that hormone treatment can alter the epigenetic state of some genes. We propose to evaluate the impact of such treatments on a genome-wide scale. This is highly relevant to human health since as many as 1 million women undergo hormone-assisted attempts at conception each year. PUBLIC HEALTH RELEVANCE: The inherited characteristics of any mammalian cell depend both upon the content of its genomic sequence and on epigenetic marks that modify the activity of genomically encoded programs. These epigenetic marks are highly dynamic during the production of germ cells and as the cells of an early embryo begin to specialize and follow particular developmental pathways. We will examine how the patterns of epigenetic marks are erased and rewritten during germ cell development and early embryogenesis, and compare the patterns of these marks in normally conceived embryos to those seen in embryos generated via hormone-assisted reproduction. These studies will both provide important basic biological insights and shed light on possible impacts of fertility treatments that are given to as many as a million women each year.